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- PDB-1e5p: Crystal structure of aphrodisin, a sex pheromone from female hamster -
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Open data
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Basic information
Entry | Database: PDB / ID: 1e5p | ||||||
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Title | Crystal structure of aphrodisin, a sex pheromone from female hamster | ||||||
![]() | APHRODISIN | ||||||
![]() | LIPOCALIN / PHEROMONE / HAMSTER | ||||||
Function / homology | ![]() | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Vincent, F. / Brown, K. / Spinelli, S. / Cambillau, C. / Tegoni, M. | ||||||
![]() | ![]() Title: Crystal structure of aphrodisin, a sex pheromone from female hamster. Authors: Vincent, F. / Lobel, D. / Brown, K. / Spinelli, S. / Grote, P. / Breer, H. / Cambillau, C. / Tegoni, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 146 KB | Display | ![]() |
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PDB format | ![]() | 115.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 386.7 KB | Display | ![]() |
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Full document | ![]() | 396.1 KB | Display | |
Data in XML | ![]() | 13 KB | Display | |
Data in CIF | ![]() | 24.9 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1a3yS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS oper:
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Components
#1: Protein | Mass: 17389.113 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene (production host): MESOCRICETUS AURATUS APHRODISIN GENE Production host: ![]() ![]() #2: Water | ChemComp-HOH / | Compound details | FUNCTION: APHRODISIN, SECRETED IN HAMSTER VAGINAL DISCHARGE, IT FUNCTIONS AS AN APHRODISIAC ...FUNCTION: APHRODISIN | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.52 Å3/Da / Density % sol: 51 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Method: vapor diffusion / pH: 3.8 Details: PEG 8K 28%, 150MM AS, 10MM NACL PH 3.8, [P]=2.65MG/NL | ||||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS Density % sol: 51 % | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Method: vapor diffusion / pH: 3.8 | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K | |||||||||||||||
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Diffraction source | Source: ![]() ![]() ![]() | |||||||||||||||
Detector | Type: ADSC CCD / Detector: CCD / Date: Sep 15, 1999 / Details: BENT MIRROR | |||||||||||||||
Radiation | Monochromator: SI(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||
Radiation wavelength |
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Reflection | Resolution: 1.6→30 Å / Num. obs: 89441 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 2.4 % / Biso Wilson estimate: 23.77 Å2 / Rsym value: 0.099 / Net I/σ(I): 7.9 | |||||||||||||||
Reflection shell | Resolution: 1.6→1.64 Å / Redundancy: 2 % / Mean I/σ(I) obs: 2.1 / Rsym value: 0.31 / % possible all: 94 | |||||||||||||||
Reflection | *PLUS Rmerge(I) obs: 0.099 | |||||||||||||||
Reflection shell | *PLUS Rmerge(I) obs: 0.31 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1A3Y Resolution: 1.63→15 Å / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.123 / ESU R Free: 0.098 Details: SEVERAL RESIDUES ARE IN ALTERNATE CONFORMATION, AND ARE PRECEEDED BY A AND B LIKE AMET, BMET. THE PROTEIN USED TO SOLVE THE STRUCTURE HAS BEEN SELENIATED SO THE METHIONINES IN THE PDB FILE ...Details: SEVERAL RESIDUES ARE IN ALTERNATE CONFORMATION, AND ARE PRECEEDED BY A AND B LIKE AMET, BMET. THE PROTEIN USED TO SOLVE THE STRUCTURE HAS BEEN SELENIATED SO THE METHIONINES IN THE PDB FILE ARE SELENOMETHIONIES (MSE) SOME OCCUPANCIES HAVE BEEN SET TO 0 OR LESS THAN 1 BECAUSE OF LACK OF DENSITY.
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Refinement step | Cycle: LAST / Resolution: 1.63→15 Å
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Refine LS restraints |
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Software | *PLUS Name: REFMAC / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 15 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS |